Richard Buggs

Research publications

28. David Boshier and Richard J. A. Buggs.
(2014)
The potential for field studies and genomic technologies to enhance resistance and resilience of British tree populations to pests and pathogens. Forestry advance accessAbstract

This paper is the first report of the sequencing of a birch tree genome, and the testing of restriction site associated DNA markers in birch. The dwarf birch (Betula nana) genome is composed of 450 million bases. We sequenced it using Illumina technology. This generated millions of short DNA reads in pairs separated by gaps of various lengths. Enough DNA was sequenced to cover the genome sixty-six times. This data set was assembled on high performance computers at Queen Mary University of London. Restriction site associated DNA (RAD) markers were developed in collaboration with scientists at the University of Edinburgh. These allowed us to examine thousands of sites in the genome of different trees, both in dwarf birch and downy birch (Betula pubescens).

This paper contains the first test in a young polyploid of the gene-dosage hypothesis for the loss/retention of duplicated genes, with the surprising finding that even in 40 generations of evolution patterns of gene loss can be to some extent predicted, and seem to fit with patterns seen in putative ancient polyploids. Repeated patterns of duplicated-gene loss were also found among independently formed populations of the new allopolyploid species Tragopogon miscellus.

This paper forms part of a special issue of American Journal of Botany on "Methods and applications of next-generation sequencing in botany". In it, the authors review recent work in our labs on genome evolution in Tragopogon and Nicotiana allopolyploids, including work on duplicated gene loss, changes in repetitive element composition, chromosome structural changes and changes to gene expression. This work was done using Illumina and 454 sequencing technologies and the Sequenom MassArray platform.

We discovered that tissue-specific gene expression in diploid parents is relaxed upon hybridization but re-emerges in the early generations of allopolyploidy; this fits with new hypotheses about the effects of hybridisation on small-RNA-mediated regulation of gene expression.

This study, which started as an undergraduate project by Natalie Elliott, provides new insights into polyploid evolution as one of the first studies to: distinguish between homeologs and among tissues, examine young naturally occurring polyploids, and examine patterns of expression in ancestral diploid species found in the same location.

This study explored new methods for investigating allopolyploid genome evolution. A review in Philosophical Transactions of the Royal Society, cited this paper in this sentence: “First studies exploring the potential of RNAseq in non-model organisms…are promising and document the dawning of an era where high-resolution transcript-profiling in non-model organisms will become commonplace”.

This paper documents the rapid loss of duplicated genes in the plant species Tragopogon miscellus (see publication 9 below). A good summary of our results and their implications, written by other scientists in the field, can be found here.

Plant species Tragopogon miscellus and T, mirus are classic examples of recent allopolyploidization. They formed about 80 years ago in the northwestern United States, through hybridization between the introduced speces T. dubius and T. pratensis. Genome duplication made them unable to interbreed with their parental species and hence new species. This paper reports the re-synthesis of both species in the greenhouses of the University of Florida.

The first in a series of special invited reviews published
by the journal of the Southern Appalacian Botanical Society. This study
tests an long-standing hypothesis: that polyploids are less likely to
form if their parents are very closely related, compared to when they
are the products of hybridisation between more distant species. Using
molecular phylogenies from several genera, we found no overall support
for the hypothesis. We argue that this fits well with current theory.
Several other groups have recently become interested in this issue, so
this is unlikely to be the last word on the topic!

A short summary of the current prospects for good model
organisms for the study of polyploidy (presence of more than two genome
sets in the cells of an organism). The best models will be natural
species whose evolution is traceable in detail, and should also have
abundant genetic sequence data available on public databases. This was
an invited perspective on a research paper in the same Issue
documenting a newly discovered polyploid species.

This reviews many cases of hybrid zone movement in both
plant and animal systems. Hybrid zones occur when the geographic ranges
of two closely-related species meet and hybridise. Movements can occur
under a variety of conditions. I argue that these provide excellent
examples of evolution in action, and also raise important issues for
species conservation. This paper develops several new and old ideas,
perhaps the most significant being that introgression of genetic
markers can be used to trace past movements. I wrote this paper
independently in the time between graduating with my doctorate and
getting my first postdoc position.

This second major paper from my DPhil research reports a
series of reciprocal transplant experiments and glasshouse drought
experiments on diploid and hexaploid Mercurialis
annua. We expected to find that the hexaploid would be better
adapted to the dry conditions where it is found in southern Spain, than
the diploid which has a more northerly distribution. Instead we found
that the diploid was better adapted than the hexaploid to all
enviroments that we tested it in, and is more drought tolerant. This
provides an additional reason for the movement of a hybrid zone between
the two ploidal levels (see 3.)

This was the first major paper to come from my DPhil
research. It shows that when diploid and hexaploid Mercurialis annua meet, the
diploids have a huge pollination advantage due to a sexual system
difference with the hexaploids. This fits with historical data showing
that diploids have rapidly advanced down the east coast of Spain over
the past few decades. This is one of the most recent, rapid hybrid zone
movements known to science.

This provides a comprehensive review of the Mercurialis annua system, providing
the background for much of the work carried out in my supervisor's lab
over the next three years, including my DPhil. This was an invited
paper and formed part of an Issue devoted to polyploidy.

ABOUT

Richard Buggs is a scientist using genomic technologies and bioinformatics to help us conserve tree species and understand how plants evolve. His research group is currently sequencing the genome of a British ash tree to help in the fight against ash dieback. This work is funded by NERC. A podcast on this research can be found here.

Richard's evolutionary research helps us to understand the causes and effects of the development of reproductive barriers in natural populations. He is particularly interested in the role of hybridisation in the origin and extinction of species. Therefore this work can aid us as we seek to care for the biodiversity around us.

He is currently a Senior Lecturer at Queen Mary, University of London. Funded by the Natural Environment Research Council (NERC) he is working on the genetics of birch tree species in the UK. In particular, he is examining the genomic consequences of hybridisation between dwarf birch, which is rare, and other more common birch species. A draft genome sequence of dwarf birch can be found here

Richard was previously a post-doctoral research associate at the University of Florida, in the lab of Doug and Pam Soltis examining the
evolutionary genetics of plant species with different numbers of chromosome sets. He studied the rapid loss and
silencing of genes after natural whole genome duplication events.

He holds a DPhil from the University of Oxford for a doctoral thesis on
the evolutionary ecology of two closely-related plant species. He received his undergraduate education at the University of
Cambridge, where he was elected Bateman Scholar at Trinity Hall, and
gained a first class Bachelor's degree in Natural Sciences.